How to start folding a DeNovo (freestyle) puzzle?
from discussion on #global with itskimo and others Define secondary structures These are the Sheets, Helices, Loops and then freeze freeze the Sheets and Helix. Band and wiggle and it starts to bend. So help it to fold at the bends by banding between the sheets. Fold it up. Add more bands going out to the sides These extra bands helps to keep the protein flat. As the protein starts to fold help it along. Try to keep it from making a knot. Now to help the protein starts to come together, wiggle for a while at ci= 0.05. http://fold.it/portal/files/chatimg/irc_192195_1299872358.png Usually the protein gets stuck at this point but, by wiggling and getting the sheets aligned and the "repeat settle" to keep together seems to work. Now for a helix First freeze the whole protein and then unfreeze the parts we well be working on. Also unfreeze the end loops to give the helix room to form. http://fold.it/portal/files/chatimg/irc_192195_1299872637.png Next rebuild the helix That has been defined by secondary structure http://fold.it/portal/files/chatimg/irc_192195_1299872721.png After we get a nice helix we stop it. http://fold.it/portal/files/chatimg/irc_192195_1299872777.png There are lots of conflicts so we do wiggles first. Now freeze the protien and unfreeze the other side. for another helix. http://fold.it/portal/files/chatimg/irc_192195_1299872948.png On this side We well have to define the structure first as a heliix. http://fold.it/portal/files/chatimg/irc_192195_1299873034.png And then rebuild to make the helix form. http://fold.it/portal/files/chatimg/irc_192195_1299873062.png By rebuilding we can get a good helix. http://fold.it/portal/files/chatimg/irc_192195_1299873235.png Now we try to put it all together By unfreezing most of the protien but leaving the sheets frozen to keep them flat. In the middle you can see a helix that wants to be a sheet so we well redefine it and make it so. http://fold.it/portal/files/chatimg/irc_192195_1299873372.png Freeze that sheet and wiggle some more. http://fold.it/portal/files/chatimg/irc_192195_1299873499.png Hopefully the helix settle. http://fold.it/portal/files/chatimg/irc_192195_1299873544.png Some of the sheets are comming together. http://fold.it/portal/files/chatimg/irc_192195_1299873605.png Remove bans and hope it stays together http://fold.it/portal/files/chatimg/irc_192195_1299873778.png *wiggle shake sidechains and run something like tlaloc repeat seatle or a banding script like tlaloc hydro *so here it is not great but that was fast *need to take more time lineing up the sheets better. http://fold.it/portal/files/chatimg/irc_192195_1299874055.png http://fold.it/portal/files/chatimg/irc_192195_1299874341.png *was able to compact it a bit but theres still some annoying voids http://fold.it/portal/files/chatimg/irc_192195_1299874610.png *Another attemp thttp://fold.it/portal/files/chatimg/irc_192195_1299874642.png *Another with mostly sheets http://fold.it/portal/files/chatimg/irc_192195_1299874714.png *http://fold.it/portal/files/chatimg/irc_192195_1299875435.png *Could use some sheet work. once those bond well it should stabilize it alot. then a quick rebuild of the helices to coil them up a bit better http://fold.it/portal/files/chatimg/irc_192195_1299875819.png here is a way to move a helix through a frozen protien fist freeze protien and unfrees the helix and loop that you want to move to the other side thenban tio where you want it t o be and rebulid http://fold.it/portal/files/chatimg/irc_192195_1299879263.png http://fold.it/portal/files/chatimg/irc_192195_1299879296.png *if you drag it it well be more twisted but if you rebuild thru to the outher side the helix stayes more in the same stance http://fold.it/portal/files/chatimg/irc_192195_1299879542.png http://fold.it/portal/files/chatimg/irc_192195_1299879555.png http://fold.it/portal/files/chatimg/irc_192195_1299879573.png just a different way of doing it *or you could drag it around wiggle and band and unfreeze etc rebuild etc *Rebuild tries to go to where you have placed the bans even through stuff thats frozen to the other side and beyond *now the helix are next to each other http://fold.it/portal/files/chatimg/irc_192195_1299879877.png *Wiggle http://fold.it/portal/files/chatimg/irc_192195_1299883252.png http://fold.it/portal/files/chatimg/irc_192195_1299883325.png http://fold.it/portal/files/chatimg/irc_192195_1299883519.png *now the sheets are lined up better http://fold.it/portal/files/chatimg/irc_192195_1299884106.png *but the helix is misbehaving http://fold.it/portal/files/chatimg/irc_192195_1299884187.png *so a rebuild is in order http://fold.it/portal/files/chatimg/irc_192195_1299884330.png *There we are with 2 helix and nice flat sheets http://fold.it/portal/files/chatimg/irc_192195_1299884630.png http://fold.it/portal/files/chatimg/irc_192195_1299884721.png *Stretched them and rebuilt the sheets to pull them flat *Getting better at this http://fold.it/portal/files/chatimg/irc_192195_1299886443.png *still need to hide those yellow balls better *finaly nice sheets but that helix is gone wild http://fold.it/portal/files/chatimg/irc_192195_1299888670.png *Judecca's version http://fold.it/portal/files/chatimg/irc_9330_1299874447.png http://fold.it/portal/files/chatimg/irc_9330_1299874502.png **Started with the sheets. but locked them so they stayed straight and banded them into something that resembled a protein **if you'd look at most of my solutions. you'll find i always leave some bands on the sheets. and just enable and disable them when i need to keep things stable http://fold.it/portal/files/chatimg/irc_9330_1299876003.png **Makes it alot easier to do moves that would normally blow the protein apart. **Try leaving them enabled for a loop rebuild script.. or leave the sheets frozen a lot longer and band them (keeps the sheets flatter) **Stops them from curling or twisting up. when you choose unfreeze kinda depends on when you want a quick point jump. *Firejuggler's: http://fold.it/portal/files/chatimg/irc_62014_1299884770.png **Looked lined up well. nice bonds forming *Rav's:http://fold.it/portal/files/chatimg/irc_174969_1299878991.png Category:FAQ